First, let me state that I'd be pleased to be under any of their care. They are all fine physicians. So, based entirely on character and personality, I've always been a McCoy fan. You don't get much better than Bones as a character. He also had a passion for his work that was refreshing and comforting in a doctor.
My least favorite was Pulaski, mostly because she seemed like a bad copy of McCoy.

Favorite: McCoy. All-around fine practitioner, an excellent surgeon, and one hell of a counselor.

Least favorite: The Voyager's EMH. Aside from the fact I think it was stupid they went seven years without giving him a name--and him not accepting a name--other than "the doctor," I just personally found him annoying most of the time (he had his moments, but not enough of them for me).

Least Favorite: I don't know whether to say Crusher or Bashir. Crusher was just sort of bland and didn't leave much of an impression either good or bad. Bashir gets on my nerves sometimes, but he has his moments. He also gets extra credit for being the cutest doctor.

I guess I'm in a small minority here, but I really like Pulaski. She could be opinionated and stubborn sometimes, but that's part of what makes her great. Some of the greatest character moments of the series were her arguments with Picard. If she had stuck around longer and the character developed more fully, she'd be my fave.